This software provides an implementation of the "pair stochastic tree adjoining grammars (PSTAGs)" for modeling 'pseudoknot' RNA structures, which is an extension of the "pair hidden Markov models on tree structures (PHMMTSs)".

PSTAG is a novel method for structural alignment to align and predict RNA secondary structures including pseudoknots.

By structural alignment, we mean a pairwise alignment to align "an unfolded RNA sequence" into "an RNA sequence of known secondary structure".